Custom (user-defined) emission policy

.clang-format

@@ -108,6 +108,10 @@ IncludeCategories:
     Priority: 4
   - Regex: '^"checkpoint\/.*\.h"'
     Priority: 4
+  - Regex: '^"kernels\/.*\.hpp"'
+    Priority: 4
+  - Regex: '^"kernels\/.*\.h"'
+    Priority: 4
   - Regex: '^"output\/.*\.h"'
     Priority: 4
   - Regex: '^"archetypes\/.*\.h"'

.gitattributes

@@ -0,0 +1 @@
+*.mp4 filter=lfs diff=lfs merge=lfs -text

.github/workflows/cpuarch.yml

@@ -63,8 +63,10 @@ jobs:
           cmake --version
       - name: Install OpenMPI 5
         run: |
-          sudo apt-get install -y libopenmpi-dev openmpi-bin
-          mpirun --version
+          if [ "${{ matrix.mpi }}" = "ON" ]; then
+            sudo apt-get install -y libopenmpi-dev openmpi-bin
+            mpirun --version
+          fi
       - name: Configure
         run: |
           if [ "${{ matrix.mpi }}" = "ON" ]; then
@@ -87,7 +89,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pgen: [streaming, turbulence, reconnection, shock, magnetosphere, accretion, wald]
+        pgen: [streaming, turbulence, reconnection, shock, magnetosphere, accretion, wald, examples/custom_emission]
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.gitignore

@@ -40,6 +40,7 @@ venv/
 *.mov
 *.mp4
 !pgens/**/*.png
+!pgens/**/*.mp4
 
 # Accidental files
 *.xc

pgens/examples/README.md

@@ -0,0 +1,7 @@
+# Examples
+
+Problem generations in this directory are just examples demonstrating how to use some of the features of the Entity.
+
+- `custom_emission`: simple example where two particles are initialized on gyrating trajectories probabilistically emitting photons while the total energy is conserved.
+
+  https://github.com/user-attachments/assets/6c5c399a-bbab-4b93-be5f-35fed1959fcc

pgens/examples/custom_emission/custom_emission.py

@@ -0,0 +1,51 @@
+import nt2
+import matplotlib.pyplot as plt
+import numpy as np
+
+plt.rcParams["text.usetex"] = True
+
+data = nt2.Data("custom_emission")
+
+
+def plot(t, data):
+    fig = plt.figure(figsize=(8, 4), dpi=150)
+    ax1 = fig.add_subplot(121)
+    prtls = data.particles.sel(t=slice(t - 0.5, t)).load()
+    prtls.plot.scatter(
+        ax=ax1,
+        x="x",
+        y="y",
+        color=["r" if sp == 1 else "b" for sp in prtls["sp"]],
+        ec=None,
+        alpha=(1 - (t - prtls["t"]) / 0.5) ** 2,
+        s=(1 - (t - prtls["t"]) / 0.5) * 5,
+    )
+    ax1.set(xlabel=r"$x$", ylabel=r"$y$", xlim=(-1, 1), ylim=(-1, 1), aspect=1)
+
+    ax2 = fig.add_subplot(122)
+    prtls1 = data.particles.sel(sp=1, t=slice(None, t)).load()
+    prtls2 = data.particles.sel(sp=2, t=slice(None, t)).load()
+    e1 = (
+        prtls1.assign(
+            e=np.sqrt(1 + prtls1["ux"] ** 2 + prtls1["uy"] ** 2 + prtls1["uz"] ** 2)
+        )
+        .groupby("t", as_index=False)["e"]
+        .sum()
+    )
+    e2 = (
+        prtls2.assign(
+            e=np.sqrt(prtls2["ux"] ** 2 + prtls2["uy"] ** 2 + prtls2["uz"] ** 2)
+        )
+        .groupby("t", as_index=False)["e"]
+        .sum()
+    )
+    e = e1.merge(e2, on="t", how="outer", suffixes=("_1", "_2")).fillna(0)
+    ax2.plot(e.t, e.e_1, label="emitters", c="r")
+    ax2.plot(e.t, e.e_2, label="emitted", c="b")
+    ax2.plot(e.t, e.e_1 + e.e_2, label="total", c="k")
+    ax2.set(xlabel=r"$t$", ylabel=r"total energy", xlim=(0, 5), ylim=(0, 3))
+    ax2.axvline(t, color="gray", ls="--")
+    ax2.legend(loc="center left")
+
+
+data.makeMovie(plot, framerate=30)

pgens/examples/custom_emission/custom_emission.toml

@@ -0,0 +1,68 @@
+[simulation]
+  name    = "custom_emission"
+  engine  = "srpic"
+  runtime = 5.0
+
+[grid]
+  resolution = [64, 64]
+  extent     = [[-1.0, 1.0], [-1.0, 1.0]]
+
+  [grid.metric]
+    metric = "minkowski"
+
+  [grid.boundaries]
+    fields    = [["PERIODIC"], ["PERIODIC"]]
+    particles = [["PERIODIC"], ["PERIODIC"]]
+
+[scales]
+  larmor0    = 0.25
+  skindepth0 = 1.0
+
+[algorithms]
+
+  [algorithms.deposit]
+    enable = false
+
+  [algorithms.timestep]
+    CFL = 0.5
+
+[particles]
+  ppc0 = 1.0
+
+  [[particles.species]]
+    label    = "p"
+    mass     = 1.0
+    charge   = 1.0
+    maxnpart = 1e2
+    emission = "custom"
+
+  [[particles.species]]
+    label    = "ph"
+    mass     = 0.0
+    charge   = 0.0
+    maxnpart = 1e4
+
+[setup]
+  x1_arr               = [0.0, 0.0]
+  x2_arr               = [0.0, 0.0]
+  x3_arr               = [0.0, 0.0]
+  ux1_arr              = [0.0, 0.0]
+  ux2_arr              = [1.0, -1.0]
+  ux3_arr              = [0.0, 0.0]
+  emission_probability = 0.05
+
+[output]
+  interval = 1
+
+  [output.fields]
+    quantities = ["N_1", "N_2", "B"]
+
+  [output.particles]
+    enable = true
+    stride = 1
+
+  [output.spectra]
+    enable = false
+
+[checkpoint]
+  keep = 0